rba_uniprot_taxonomy {rbioapi}R Documentation

Get UniProt Taxonomy Nodes

Description

Using this function, you can retrieve taxonomic nodes information by providing their NCBI taxonomic identifiers. also, you can explicitly retrieve other nodes in relation to your supplied node's hierarchy in UniProt Taxonomy database.

Usage

rba_uniprot_taxonomy(
  ids,
  hierarchy = NULL,
  node_only = TRUE,
  page_size = 200,
  page_number = 1,
  ...
)

Arguments

ids

(numeric) a single or a numeric vector of NCBI taxonomic identifier(s)

hierarchy

Retrieve taxonomic nodes that have specific hierarchical relation to your supplied taxonomic node. should be one of: "children", "parent" or "siblings".

node_only

Retrieve only the node(s) information and exclude URL links to parents, siblings and children nodes.

page_size

(numeric) Only when hierarchy is supplied. hierarchy information may be very long, thus UniProt API will paginate the results, you may use this argument to control the pagination. maximum value is 200.

page_number

(numeric) Only when hierarchy is supplied. hierarchy information may be very long, thus UniProt API will paginate the results, you may use this argument to control the pagination.

...

rbioapi option(s). See rba_options's arguments manual for more information on available options.

Value

a list containing your supplied nodes or their related nodes taxonomic information.

Corresponding API Resources

"GET https://ebi.ac.uk/proteins/api/ids/{ids}"
"GET https://ebi.ac.uk/proteins/api/ids/id/{id}/node"
"GET https://ebi.ac.uk/proteins/api/id/{id}/node"
"GET https://ebi.ac.uk/proteins/api/id/{id}/children"
"GET https://ebi.ac.uk/proteins/api/id/{id}/children/node"
"GET https://ebi.ac.uk/proteins/api/id/{id}/parent"
"GET https://ebi.ac.uk/proteins/api/id/{id}/parent/node"
"GET https://ebi.ac.uk/proteins/api/id/{id}/siblings"
"GET https://ebi.ac.uk/proteins/api/id/{id}/siblings/node"

References

See Also

Other "UniProt - Taxonomy": rba_uniprot_taxonomy_lca(), rba_uniprot_taxonomy_lineage(), rba_uniprot_taxonomy_name(), rba_uniprot_taxonomy_path(), rba_uniprot_taxonomy_relationship()

Examples


rba_uniprot_taxonomy(ids = c(9606, 10090))


rba_uniprot_taxonomy(ids = 9989, hierarchy = "children")



[Package rbioapi version 0.8.1 Index]